We were also interested in seeing how using unsupervised methods to determine classes would change the results.
We identified a MLL translocation-specific (379 probes) signature and a phenotype-specific (622 probes) signature which have been tested using unsupervised methods.
We had also tried to apply the methods in [ 33] on this dataset but could not differentiate the IBD samples with other samples using unsupervised methods.
Using unsupervised methods, cancer patients were separated into distinct groups based on gene expression patterns in one of the following pathways: apoptosis, cell cycle, angiogenesis, metastasis, p53, DNA repair, and several receptor-mediated signaling pathways including chemokines, EGF, FGF, HIF, MAP kinase, JAK and NF-κB.
CENTIPEDE [ 24] used unsupervised methods to integrate TF-DNA intepigeneticepigenetic and evolutionary data, and is most similar to our efforts.
Besides clustering, one can use unsupervised methods like PCA analysis to explore the binding pattern across conditions.
To date, class discovery studies have used unsupervised methods, especially cluster analysis, to 'discover' sample or gene groupings.
Furthermore, databases such as KEGG use unsupervised methods to cluster genes into ortholog groups that may not track with protein function (Schnoes et al., 2009).
We first consider PCA, the most commonly used unsupervised method.
In constructing a workflow to map the binding sites of the currently characterized structural proteome, we adopted a modular approach that comprises objective binding site detection, binding site comparison (BSC), mapping of detected binding sites using unsupervised learning methods, and visualization of binding site maps.
